In 1968 the University started to function on the new campus at Msida (Tal-Qroqq), and the need was felt for a full-time chaplain. Before January 1971 the ecclesiastical assistant to the University Students' Catholic Guild, later the "Moviment Kattoliku Studenti Universitarji," used to act as chaplain to the students. In this capacity Mgr Salv Grima, Fr Robert Darmanin sj and Fr Joseph Bernard sj served the spiritual needs of the university students. These were nominated by the Archbishop alone since they were ecclesiastical assistants to a Catholic group. Fr Mario Jaccarini sj was the first official full-time chaplain, nominated by both the Archbishop and the University authorities to serve not only the students but all the university staff: academic, administrative and technical.

Fr Mario Jaccarini sj ended his term as chaplain in 1980. Fr Alfred Micallef sj, who had been chaplain at the Malta College of Arts, Science and Technology (MCAST), Msida, took over when he came to Tal-Qroqq with the students of MCAST after it was integrated with the University. He was chaplain till 1986. Fr Paul Pace sj was chaplain from 1986 to 1991. Though when, in 1989, he needed to spend one year in Canada, Fr Jaccarini sj stood in for him. Fr Robert Wirth was chaplain from 1991 to 1995, while Fr Philip Chircop sj was chaplain from 1995 to 1997. Fr Authur G. Vella sj was acting-chaplain in 1997 and 1998. Fr Jimmy Bartolo sj took over in October 1998 and completed his term in June 2008. Fr Michael Bugeja sj has been in office as chaplain since July 2008. He was absent between August 2013 and May 2014 as he was completing his final year of formation, known as the tertianship, in the Philippines. During this time, Fr Patrick Magro sj took over as Chaplain. In 2011, the Chaplaincy team mourned Fr Mario Jaccarini's (1928 - 2011) passing.

During Fr Jaccarini's term of office, the chapel and the whole chaplaincy complex started to be built. The planning committee was made up of the Rector Prof. Edwin Borg Costanzi, Fr Peter Serracino Inglott, Fr Mario Jaccarini, Mr Vincent DeGaetano (President of the Catholic Guild) and Mr Lino Gatt, who designed the chapel and its adjacent buildings. Mr Lino Gatt tried to keep the terraced formation of the fields on which the Chapel is built. The first stone was blessed and laid on 26th January, 1977 by His Grace Archbishop Michael Gonzi, who took great interest in the project and who had supplied the funds for the building together with LM1000 donated by His Holiness Pope Paul VI. The University Students Catholic Movement suggested that the patron saint of the Chapel be St Thomas More since he was a married layman, engaged in public life as a lawyer, a judge, and Lord Chancellor to King Henry VIII. He was also a man who was ready to sacrifice everything for his principles and for God.

The University Chapel of St Thomas More, though designed by Mr L. Gatt, was built by the university architect, Mr William Micallef. It started functioning, although still incomplete, in 1978. In successive years, it underwent various refurbishments such as the one in anticipation of H.H. Pope John Paul II's visit (1990).